■ PAUSE POINT Purified PCR product can be stored at –20 °C overnight or longer. 124Nextera XT DNA sample preparation kit. According to the manufacturer's protocol, generate Miseq sequencing-ready libraries with unique bar codes for each sample.125Sequence the samples prepared in Step 124 on the Illumina Miseq according to the Illumina user manual.126Analyze sequencing data. By using the expected reference genome sequence, perform indel analysis with read alignment programs such as ClustalW (http://www.clustal.org/), Geneious (http://www.geneious.com/) or by simple sequence analysis scripts.
